3ZYV

Crystal structure of the mouse liver Aldehyde Oxidase 3 (mAOX3)

PDB DOI: https://doi.org/10.2210/pdb3ZYV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mus musculus
Mutation(s): No

Deposited: 2011-08-27 Released: 2012-09-05
Deposition Author(s): Trincao, J., Coelho, C., Mahro, M., Rodrigues, D., Terao, M., Garattini, E., Leimkuehler, S., Romao, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free: 0.285
R-Value Work: 0.256
R-Value Observed: 0.257

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The First Mammalian Aldehyde Oxidase Crystal Structure: Insights Into Substrate Specificity.

Coelho, C., Mahro, M., Trincao, J., Carvalho, A.T.P., Ramos, M.J., Terao, M., Garattini, E., Leimkuhler, S., Romao, M.J.

(2012) J Biol Chem 287: 40690

PubMed: 23019336 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1074/jbc.M112.390419
Primary Citation of Related Structures:
3ZYV

PubMed Abstract:
Aldehyde oxidases have pharmacological relevance, and AOX3 is the major drug-metabolizing enzyme in rodents.

Organizational Affiliation

Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.

Macromolecule Content

Total Structure Weight: 595.23 kDa
Atom Count: 38,315
Modelled Residue Count: 5,016
Deposited Residue Count: 5,340
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AOX3	A, B, C, D	1,335	Mus musculus	Mutation(s): 0 EC: 1.2.3.1
UniProt
Find proteins for G3X982 (Mus musculus) Explore G3X982 Go to UniProtKB: G3X982
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G3X982
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C]	BA [auth D], J [auth A], P [auth B], V [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain BA [auth D] Focus chain J [auth A] Focus chain P [auth B] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain J [auth A] Focus chain P [auth B] Focus chain V [auth C]
MTE Query on MTE Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain Z [auth D] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D]	H [auth A], N [auth B], T [auth C], Z [auth D]	PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER C₁₀ H₁₄ N₅ O₆ P S₂ HPEUEJRPDGMIMY-IFQPEPLCSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain H [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D]	F [auth A] G [auth A] L [auth B] M [auth B] R [auth C] F [auth A], G [auth A], L [auth B], M [auth B], R [auth C], S [auth C], X [auth D], Y [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth D] Focus chain Y [auth D]
MOS Query on MOS Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C]	AA [auth D], I [auth A], O [auth B], U [auth C]	DIOXOTHIOMOLYBDENUM(VI) ION H Mo O₂ S BDSRWPHSAKXXRG-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth D]	E [auth A], K [auth B], Q [auth C], W [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free: 0.285
R-Value Work: 0.256
R-Value Observed: 0.257
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.88	α = 78.16
b = 135.27	β = 77.72
c = 147.37	γ = 89.9

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-09-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-09-05
Type: Initial release
Version 1.1: 2013-04-10
Changes: Database references
Version 1.2: 2013-04-24
Changes: Structure summary
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description